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Classification of unknown primary tumors with a data-driven method based on a large microarray reference database

Kalle A Ojala, Sami K Kilpinen and Olli P Kallioniemi*

Author Affiliations

Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00140 Helsinki, Finland

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Genome Medicine 2011, 3:63  doi:10.1186/gm279

Published: 17 October 2011

Abstract

We present a new method to analyze cancer of unknown primary origin (CUP) samples. Our method achieves good results with classification accuracy (88% leave-one-out cross validation for primary tumors from 56 categories, 78% for CUP samples), and can also be used to study CUP samples on a gene-by-gene basis. It is not tied to any a priori defined gene set as many previous methods, and is adaptable to emerging new information.